Structure of PDB 6gc7 Chain J Binding Site BS01

Receptor Information

>6gc7 Chain J (length=142) Species: 83333 (Escherichia coli K-12)

MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDT
GDYIIVLNADKVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERV
IEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI

Ligand information

>6gc7 Chain A (length=1901)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccgguggugaaaggccaaucaa
accgggagauagcugguucuccccgaaagcuauuuagguagcgccucgug
aauucaucuccggggguagagcaccaaacugcgaauaccggagaauguua
ucacgggagacacacggcgggugcuaacguccgucgugaagagggaaaca
acccagaccgccagcuaaggucccaaagucaugguuaagugggaaacgcg
gaagauguaacggggcuaaaccaugcaccgaagcugcggcagcgacgcuu
augcguuguuggguaggggagcguucuguaagccugcgaaggugugcugu
gaggcaugcuggagguaucagaagugcgaaugcugacauaaguaacgaua
aagcgggugaaaagcccgcucgccggaagaccaaggguuccuguccaacg
uuaaucggggcagggugagucgaccccuaaggcgaggccgaaaggcguag
ucgaugggaaacagguuaauauuccuguacuugguguuacugcgaagggg
ggacggagaaggcuauguuggccgggcgacgguugucccgguuuaagcgu
guaggcugguuuuccaggcaaauccggaaaaucaaggcugaggcgugaug
acgaggcacuacggugcugaagcaacaaaugcccugcuuccaggaaaagc
cucuaagcaucagguaacaucaaaucguaccccaaaccgacacagguggu
cagguagagaauaccaaggcgcuugagagaacucgggugaaggaacuagg
caaaauggugccggcacgcugauauguaggugaggucccucgcggaugga
gcugaaaucagucgaagauaccagcuggcgccaggcugucuccacccgag
acucagugaaauugaacucgcugugaagaugcaguguacccgcggcaaga
cggaaaucccuaucugccgugggcgcuggagaacugaggggggcugcucc
uaguacgagaggaccggaguggacgcaucacugguguucggguugucaug
ccaauggcacugcccgguagcuaaaugcggaagagauaagugcugaaagc
aucuaagcacgaaacuugccccgagaugaguucucccugacccuuuaagg
guccugaaggaacguugaagacgacgacguugauaggccggguguguaag
cgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaacc
u

<<<<<<<<......<<<<<<<<<<<....<.<<.<<<<<<<<<<<<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<......>..<<<<<<.....<<....
.>>....>>>>>>..<<<..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>.>..>>>
>>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<......>>>>>..>>>......>>.>>>>>>>.>>.....
..........<<....>>....>>.........<<<.......>>>....
.........>....>>>>>>>>>>>.......<<<<..<<<<<......>
>>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<...<<<<<<.<<.....>>.......
>>>>>>......>.>>..<<<<<<....<<<<<....>>>>>..<<<<<<
<...<<<<<<<<<......<<.......>>.......>>>>>>.>>>...
>>>>>>>.....<<<<<<<<<<......>>>>>>>>>>....<<<.....
.>>>...<<<<.<<<...<<<(((.....<<<<<<...........<..>
...........))).....>>>>>>.>>>...>>>>>>><<<.<..<...
...>..>.>>>....>>>>>><<<<<<<...<<<......<<<<<<<<..
..>>>>>>>>...>>>..>>>>>.>>.....>>>>>><......<<....
.<<<<<<.......>>>>>><<<<....<<.<<.<<...<<<<<<...<<
.....>>.>>>>>>....((<<<.<<<...<<....<<<....>>>....
>>...>>>...<<<<........>>>>.))<<<<<<<<<<<<<...<<<<
....<<<<..<<<..<<<<<<<<<<<....(((...>>>>>><<..<<<<
...<<<<<<<<<<<<.<<.....>>>>>>>>>>..>>>>...>>>>...>
><..<<<<<....>>>>>...>>>>>>...>>>...>>>>.........>
>>>...>>....>>>>>>>>>>>.>>>..>>.....<<......>>>>.>
>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<<........
.......<<<<..>>>><<<<<......<<<...<<<<.....>>>>...
>>>....>>>>>............<<<<..>>>>.....>>.>>>>>>>>
.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<<.<<<
.<.......>..>>>>>>>>>>>....<<<<<<<...<<<<..<<<<<<<
...............>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<)
)).>>>>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<......
.....>>>>>....>>>.>>>>.......>>>>>>>..<<<<<.....>>
>>>.....<<..<<<<<.......>>>>>....<<<<<<<<..<<....<
<<<<....>>>>>...>>...>>>>>.>>>.....>>.....>>>>>>>>
.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gc7 Structural Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution.
• Resolution: 4.3 Å
• Binding residue (original residue number in PDB): K2 T3 T5 K7 W15 G26 R27 T30 R37 K39 H47 Y53 T65 K68 Y74 Y75 H76 T78 H80 I81 G82 I84 K85 R96 E102 A104 M108 P110 P113 L114 R116 R120 N131 A134 Q135 Q136
• Binding residue (residue number reindexed from 1): K2 T3 T5 K7 W15 G26 R27 T30 R37 K39 H47 Y53 T65 K68 Y74 Y75 H76 T78 H80 I81 G82 I84 K85 R96 E102 A104 M108 P110 P113 L114 R116 R120 N131 A134 Q135 Q136

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0048027 mRNA 5'-UTR binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6gc7, PDBe:6gc7, PDBj:6gc7
• PDBsum: 6gc7
• PubMed: 29883607
• UniProt: P0AA10|RL13_ECOLI Large ribosomal subunit protein uL13 (Gene Name=rplM)